예제 #1
0
    void VideoWriter_ufmf::setupOutputFile(StampedImage stampedImg) 
    {

        // Set error control state, set exceptions mask
        file_.clear();
        file_.exceptions(std::ifstream::failbit | std::ifstream::badbit);

        // Get unique name for file and open for reading
        QString incrFileName = getUniqueFileName();

        try
        {
            file_.open(incrFileName.toStdString(), std::ios::binary | std::ios::out);
        }
        catch (std::ifstream::failure &exc)
        {
            unsigned int errorId = ERROR_VIDEO_WRITER_INITIALIZE;
            std::string errorMsg("video writer unable to open file:\n\n"); 
            errorMsg += exc.what();
            throw RuntimeError(errorId, errorMsg); 
        }

        if (!file_.is_open())
        {
            unsigned int errorId = ERROR_VIDEO_WRITER_INITIALIZE;
            std::string errorMsg("video writer unable to open file:\n\n"); 
            errorMsg += "no exception thrown";
            throw RuntimeError(errorId, errorMsg); 
        }
        setSize(stampedImg.image.size());

    }
예제 #2
0
int main(int argc, char **argv) {

  embInitPV("kdnapenny", argc, argv, "KBWS", "1.0.8");

  struct soap soap;
  char* jobid;
  char* result;

  AjPSeqall  seqall;
  AjPSeq     seq;
  AjPFile    outf;
  AjPStr     substr;
  AjPStr     inseq = NULL;

  seqall = ajAcdGetSeqall("seqall");
  outf   = ajAcdGetOutfile("outfile");

  AjPStr    tmp         = NULL;
  AjPStr    tmpFileName = NULL;
  AjPSeqout fil_file;
  AjPStr    line        = NULL;
  AjPStr    sizestr     = NULL;
  ajint     thissize    = 0;
  ajint     nb          = 0;
  AjBool    are_prot    = ajFalse;
  ajint     size        = 0;
  AjPFile   infile;

  tmp = ajStrNewC("fasta");

  fil_file    = ajSeqoutNew();
  tmpFileName = getUniqueFileName();

  if( !ajSeqoutOpenFilename(fil_file, tmpFileName) ) {
    embExitBad();
  }

  ajSeqoutSetFormatS(fil_file, tmp);

  while (ajSeqallNext(seqall, &seq)) {
    if (!nb) {
      are_prot  = ajSeqIsProt(seq);
    }
    ajSeqoutWriteSeq(fil_file, seq);
    ++nb;
  }
  ajSeqoutClose(fil_file);
  ajSeqoutDel(&fil_file);

  if (nb < 2) {
    ajFatal("Multiple alignments need at least two sequences");
  }

  infile = ajFileNewInNameS(tmpFileName);

  while (ajReadline(infile, &line)) {
    ajStrAppendS(&inseq,line);
    ajStrAppendC(&inseq,"\n");
  }

  soap_init(&soap);

  char* in0;
  in0 = ajCharNewS(inseq);
  if ( soap_call_ns1__runDnapenny( &soap, NULL, NULL, in0, &jobid ) == SOAP_OK ) {
    fprintf(stderr,"Jobid: %s\n",jobid);
  } else {
    soap_print_fault(&soap, stderr);
  }

  int check = 0;
  while ( check == 0 ) {
    if ( soap_call_ns1__checkStatus( &soap, NULL, NULL, jobid,  &check ) == SOAP_OK ) {
      fprintf(stderr,"*");
    } else {
      soap_print_fault(&soap, stderr);
    }
    sleep(3);
  }
  fprintf(stderr, "\n");

  if ( soap_call_ns1__getResult( &soap, NULL, NULL, jobid,  &result ) == SOAP_OK ) {
    substr = ajStrNewC(result);
    ajFmtPrintF(outf,"%S\n",substr);
  } else {
    soap_print_fault(&soap, stderr);
  }

  ajSysFileUnlinkS(tmpFileName);

  soap_destroy(&soap);
  soap_end(&soap);
  soap_done(&soap);

  ajFileClose(&outf);
  ajSeqallDel(&seqall);
  ajSeqDel(&seq);
  ajStrDel(&substr);

  embExit();

  return 0;
}
예제 #3
0
int main(int argc, char **argv) {
  // initialize EMBASSY info
  embInitPV("kweblogo", argc, argv, "KBWS", "1.0.9");

  // soap driver and parameter object
  struct soap soap;
  struct ns1__weblogoInputParams params;

  char* jobid;

  AjPSeqall seqall;
  AjPSeq    seq;
  AjPStr    substr;
  AjPStr    inseq = NULL;

  // get input sequence
  seqall= ajAcdGetSeqall("seqall");

  // get/set parameters
  params.format = ajCharNewS(ajAcdGetString("format"));

  AjPStr     tmp= NULL;
  AjPStr     tmpFileName= NULL;
  AjPSeqout  fil_file;
  AjPStr     line= NULL; /* if "AjPStr line; -> ajReadline is not success!" */
  AjPStr sizestr= NULL;
  ajint thissize;

  ajint   nb= 0;
  AjBool  are_prot= ajFalse;
  ajint   size= 0;
  AjPFile infile;

  AjPFile goutf;
  AjPStr  goutfile;

  goutfile= ajAcdGetString("goutfile");

  tmp= ajStrNewC("fasta");

  fil_file= ajSeqoutNew();
  tmpFileName= getUniqueFileName();

  if(!ajSeqoutOpenFilename(fil_file, tmpFileName)) {
    embExitBad();
  }

  ajSeqoutSetFormatS(fil_file, tmp);

  while (ajSeqallNext(seqall, &seq)) {
    if (!nb) {
      are_prot  = ajSeqIsProt(seq);
    }
    ajSeqoutWriteSeq(fil_file, seq);
    ++nb;
  }
  ajSeqoutClose(fil_file);
  ajSeqoutDel(&fil_file);

  if (nb < 2) {
    ajFatal("Multiple alignments need at least two sequences");
  }

  infile = ajFileNewInNameS(tmpFileName);

  while (ajReadline(infile, &line)) {
    ajStrAppendS(&inseq,line);
    ajStrAppendC(&inseq,"\n");
  }

  soap_init(&soap);

  char* in0;
  in0= ajCharNewS(inseq);
  if (soap_call_ns1__runWeblogo( &soap, NULL, NULL, in0, &params, &jobid) == SOAP_OK) {
  } else {
    soap_print_fault(&soap, stderr);
  }

  int check= 0;
  while (check == 0 ) {
    if (soap_call_ns1__checkStatus(&soap, NULL, NULL, jobid,  &check) == SOAP_OK) {
    } else {
      soap_print_fault(&soap, stderr);
    }
    sleep(3);
  }

  char* image_url;
  if (soap_call_ns1__getResult(&soap, NULL, NULL, jobid,  &image_url) == SOAP_OK) {
    goutf= ajFileNewOutNameS(goutfile);

    if (!goutf) {
      // can not open image output file
      ajFmtError("Problem writing out image file");
      embExitBad();
    }

    if (!gHttpGetBinC(image_url, &goutf)) {
      // can not download image file
      ajFmtError("Problem downloading image file");
      embExitBad();
    }
  } else {
    soap_print_fault(&soap, stderr);
  }

  // delete temporary multi-fasta sequence file
  ajSysFileUnlinkS(tmpFileName);

  // destruct SOAP driver
  soap_destroy(&soap);
  soap_end(&soap);
  soap_done(&soap);

  // destruct EMBOSS object
  ajSeqallDel(&seqall);
  ajSeqDel(&seq);
  ajStrDel(&substr);

  // exit
  embExit();

  return 0;
}
예제 #4
0
    int main(int argc, char **argv) {

    embInitPV("kmafft", argc, argv, "KBWS", "1.0.8");

    struct soap soap;
    struct ns1__mafftInputParams params;
    char* jobid;
    char* result;

    AjPSeqall  seqall;
    AjPSeq     seq;
    AjPFile    outf;
    AjPStr     substr;
    AjPStr     inseq = NULL;
    AjPStr     strategy;
    AjPStr     outorder;
    float      op;
    float      ep;
    AjPStr     scorematrix;
    AjBool     homologs;
    AjBool     showhomologs;
    float      threshold;
    AjPStr     referenceseq;
    AjPStr     harrplot;

    strategy     =      ajAcdGetString("strategy");
    outorder     =      ajAcdGetString("outorder");
    op           =      ajAcdGetFloat("op");
    ep           =      ajAcdGetFloat("ep");
    scorematrix  =      ajAcdGetString("scorematrix");
    homologs     =      ajAcdGetBoolean("homologs");
    showhomologs =      ajAcdGetBoolean("showhomologs");
    threshold    =      ajAcdGetFloat("threshold");
    referenceseq =      ajAcdGetString("referenceseq");
    harrplot     =      ajAcdGetString("harrplot");

    seqall = ajAcdGetSeqall("seqall");
    outf   = ajAcdGetOutfile("outfile");

    params.strategy = ajCharNewS(strategy);
    params.outorder = ajCharNewS(outorder);
    params.op = op;
    params.ep = ep;
    params.scorematrix = ajCharNewS(scorematrix);
    if (homologs) {
      params.homologs = xsd__boolean__true_;
    } else {
      params.homologs = xsd__boolean__false_;
    }
    if (showhomologs) {
      params.showhomologs = xsd__boolean__true_;
    } else {
      params.showhomologs = xsd__boolean__false_;
    }
    params.threshold = threshold;
    params.referenceseq = ajCharNewS(referenceseq);
    params.harrplot = ajCharNewS(harrplot);

    AjPStr     tmp         = NULL;
    AjPStr     tmpFileName = NULL;
    AjPSeqout  fil_file;
    AjPStr     line        = NULL; /* if "AjPStr line; -> ajReadline is not success!" */
    AjPStr     sizestr     = NULL;
    ajint      thissize;

    ajint      nb       = 0;
    AjBool     are_prot = ajFalse;
    ajint      size     = 0;
    AjPFile    infile;

    tmp = ajStrNewC("fasta");

    fil_file = ajSeqoutNew();
    tmpFileName = getUniqueFileName();

    if( !ajSeqoutOpenFilename(fil_file, tmpFileName) ) {
        embExitBad();
    }

    ajSeqoutSetFormatS(fil_file, tmp);

    while (ajSeqallNext(seqall, &seq)) {
      if (!nb) {
        are_prot  = ajSeqIsProt(seq);
    }
      ajSeqoutWriteSeq(fil_file, seq);
      ++nb;
    }
    ajSeqoutClose(fil_file);
    ajSeqoutDel(&fil_file);

    if (nb < 2) {
        ajFatal("Multiple alignments need at least two sequences");
    }

    infile = ajFileNewInNameS(tmpFileName);

    while (ajReadline(infile, &line)) {
      ajStrAppendS(&inseq,line);
      ajStrAppendC(&inseq,"\n");
    }

    soap_init(&soap);

    char* in0;
    in0 = ajCharNewS(inseq);
    if ( soap_call_ns1__runMafft( &soap, NULL, NULL, in0, &params, &jobid ) == SOAP_OK ) {
      fprintf(stderr,"Jobid: %s\n",jobid);
    } else {
      soap_print_fault(&soap, stderr);
    }

    int check = 0;
    while ( check == 0 ) {
      if ( soap_call_ns1__checkStatus( &soap, NULL, NULL, jobid,  &check ) == SOAP_OK ) {
        fprintf(stderr,"*");
      } else {
        soap_print_fault(&soap, stderr);
      }
      sleep(3);
    }

    fprintf(stderr,"\n");

    if ( soap_call_ns1__getResult( &soap, NULL, NULL, jobid,  &result ) == SOAP_OK ) {
      substr = ajStrNewC(result);
      ajFmtPrintF(outf,"%S\n",substr);
    } else {
      soap_print_fault(&soap, stderr);
    }

    ajSysFileUnlinkS(tmpFileName);

    soap_destroy(&soap);
    soap_end(&soap);
    soap_done(&soap);

    ajFileClose(&outf);

    ajSeqallDel(&seqall);
    ajSeqDel(&seq);
    ajStrDel(&substr);

    embExit();

    return 0;
}
예제 #5
0
int main(int argc, char **argv) {

  embInitPV("kclustalw", argc, argv, "KBWS", "1.0.8");

  struct soap soap;
  struct ns1__clustalwInputParams params;
  char* jobid;
  char* result;

  AjPSeqall  seqall;
  AjPSeq     seq;
  AjPFile    outf;
  AjPFile    outf_dnd;
  AjPStr     substr;
  AjPStr     inseq = NULL;
  AjPStr     alignment;
  AjPStr     output;
  AjPStr     matrix;
  AjPStr     outorder;
  ajint      ktup;
  ajint      window;
  ajint      gapopen;
  float      gapext;
  ajint      gapdist;
  AjBool     endgaps;
  ajint      pairgap;
  ajint      topdiags;
  AjPStr     score;
  AjBool     tossgaps;
  AjBool     kimura;
  AjPStr     outputtree;
  AjBool     tree;
  AjBool     quicktree;
  AjBool     align;
  AjPStr     clustering;
  ajint      numiter;
  AjPStr     iteration;
  alignment  = ajAcdGetString("alignment");
  output     = ajAcdGetString("output");
  matrix     = ajAcdGetString("matrix");
  outorder   = ajAcdGetString("outorder");
  ktup       = ajAcdGetInt("ktup");
  window     = ajAcdGetInt("window");
  gapopen    = ajAcdGetInt("gapopen");
  gapext     = ajAcdGetFloat("gapext");
  gapdist    = ajAcdGetInt("gapdist");
  endgaps    = ajAcdGetBoolean("endgaps");
  pairgap    = ajAcdGetInt("pairgap");
  topdiags   = ajAcdGetInt("topdiags");
  score      = ajAcdGetString("score");
  tossgaps   = ajAcdGetBoolean("tossgaps");
  kimura     = ajAcdGetBoolean("kimura");
  outputtree = ajAcdGetString("outputtree");
  tree       = ajAcdGetBoolean("tree");
  quicktree  = ajAcdGetBoolean("quicktree");
  align      = ajAcdGetBoolean("align");
  clustering = ajAcdGetString("clustering");
  numiter    = ajAcdGetInt("numiter");
  iteration  = ajAcdGetString("iteration");

  seqall = ajAcdGetSeqall("seqall");
  outf   = ajAcdGetOutfile("outfile");
  outf_dnd = ajAcdGetOutfile("dndoutfile");
  params.alignment = ajCharNewS(alignment);
  params.output = ajCharNewS(output);
  params.matrix = ajCharNewS(matrix);
  params.outorder = ajCharNewS(outorder);
  params.ktup = ktup;
  params.window = window;
  params.gapopen = gapopen;
  params.gapext = gapext;
  params.gapdist = gapdist;
  if (endgaps) {
    params.endgaps = xsd__boolean__true_;
  } else {
    params.endgaps = xsd__boolean__false_;
  }
  params.pairgap = pairgap;
  params.topdiags = topdiags;
  params.score = ajCharNewS(score);

  if (tossgaps) {
    params.tossgaps = xsd__boolean__true_;
  } else {
    params.tossgaps = xsd__boolean__false_;
  }
  if (kimura) {
    params.kimura = xsd__boolean__true_;
  } else {
    params.kimura = xsd__boolean__false_;
  }
  params.outputtree = ajCharNewS(outputtree);
  if (tree) {
    params.tree = xsd__boolean__true_;
  } else {
    params.tree = xsd__boolean__false_;
  }
  if (quicktree) {
    params.quicktree = xsd__boolean__true_;
  } else {
    params.quicktree = xsd__boolean__false_;
  }
  if (align) {
    params.align = xsd__boolean__true_;
  } else {
    params.align = xsd__boolean__false_;
  }
  params.clustering = ajCharNewS(clustering);
  params.numiter = numiter;
  params.iteration = ajCharNewS(iteration);

  AjPStr     tmp = NULL;
  AjPStr     tmpFileName = NULL;
  AjPSeqout  fil_file;
  AjPStr     line = NULL; /* if "AjPStr line; -> ajReadline is not success!" */
  AjPStr sizestr = NULL;
  ajint thissize;

  ajint      nb = 0;
  AjBool     are_prot = ajFalse;
  ajint      size = 0;
  AjPFile    infile;

  tmp = ajStrNewC("fasta");

  fil_file = ajSeqoutNew();
  tmpFileName = getUniqueFileName();

  if( !ajSeqoutOpenFilename(fil_file, tmpFileName) ) {
    embExitBad();
  }

  ajSeqoutSetFormatS(fil_file, tmp);

  while (ajSeqallNext(seqall, &seq)) {
    if (!nb) {
      are_prot  = ajSeqIsProt(seq);
    }
    ajSeqoutWriteSeq(fil_file, seq);
    ++nb;
  }
  ajSeqoutClose(fil_file);
  ajSeqoutDel(&fil_file);

  if (nb < 2) {
    ajFatal("Multiple alignments need at least two sequences");
  }

  infile = ajFileNewInNameS(tmpFileName);

  while (ajReadline(infile, &line)) {
    ajStrAppendS(&inseq,line);
    ajStrAppendC(&inseq,"\n");
  }

  soap_init(&soap);

  char* in0;
  in0 = ajCharNewS(inseq);
  if ( soap_call_ns1__runClustalw( &soap, NULL, NULL, in0, &params, &jobid ) == SOAP_OK ) {
    fprintf(stderr,"Jobid: %s\n",jobid);
  } else {
    soap_print_fault(&soap, stderr);
  }

  int check = 0;
  while ( check == 0 ) {
    if ( soap_call_ns1__checkStatus( &soap, NULL, NULL, jobid,  &check ) == SOAP_OK ) {
      fprintf(stderr,"*");
    } else {
      soap_print_fault(&soap, stderr);
    }
    sleep(3);
  }
  fprintf(stderr,"\n");

  char* type;

  type = "out";
  if(soap_call_ns1__getMultiResult( &soap, NULL, NULL, jobid, type, &result )== SOAP_OK) {
    substr = ajStrNewC(result);
    fprintf(stdout, "%s\n", ajStrGetPtr(substr));
  } else {
    soap_print_fault(&soap, stderr);
  }

  type = "aln";
  if(soap_call_ns1__getMultiResult( &soap, NULL, NULL, jobid, type, &result )== SOAP_OK) {
    substr = ajStrNewC(result);
    ajFmtPrintF(outf,"%S\n",substr);
  } else {
    soap_print_fault(&soap, stderr); 
  }

  type = "dnd";
  if(soap_call_ns1__getMultiResult( &soap, NULL, NULL, jobid, type, &result )== SOAP_OK) {
    substr = ajStrNewC(result);
    ajFmtPrintF(outf_dnd,"%S\n",substr);
  } else {
    soap_print_fault(&soap, stderr); 
  }


  ajSysFileUnlinkS(tmpFileName);

  soap_destroy(&soap);
  soap_end(&soap);
  soap_done(&soap);

  ajFileClose(&outf_dnd);

  ajFileClose(&outf);

  ajSeqallDel(&seqall);
  ajSeqDel(&seq);
  ajStrDel(&substr);

  embExit();

  return 0;
}